Churches hold the balance of power in nearly two-thirds of local authority education committees due to a law which compels councils to appoint three religious representatives, according to a coalition of cross-party politicians and secular groups.
Schools are also compelled to promote children's "spiritual development" through religious observance unless parents opt out.
Holyrood's Education and Culture Committee will consider two separate petitions to reform these practices.
The Edinburgh Secular Society (ESS) has petitioned for a repeal of section 124 of the Local Government Act, which ensures religious representation on council education boards.
Recent census results show that nearly half of Scots profess no religious beliefs, meaning "undemocratic, unelected, unscientific and self-serving" church leaders should not have the legal right to make decisions on school education, according to ESS.
Their view is backed by Green MSP Patrick Harvie amid concerns about the promotion of creationism in schools, and SNP councillor Sandy Howat, who said churches' "undemocratic influence over public education is fundamentally at odds with the principles of respect, equality and shared freedoms".
Meanwhile, Secular Scotland has lodged a separate petition to amend the Education (Scotland) Act 1980 to make religious observance an "opt-in" activity rather than an "opt-out".
Holyrood's Public Petitions Committee has unanimously agreed to the Education Committee's request to refer the ESS petition to them for consideration alongside the Secular Scotland petition, which was referred to them at an earlier date.